How is the Users folder linked? Is it a hard link or symlink? I believe you can use BitLocker to encrypt A: if you use a hard link it might ask for a password when you startup. Just a theory.
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wolfo9999Aug 17 '13 at 19:12

Why would you want to encrypt a whole drive? Afterwards access times could be terrible, since you need to decrypt every time you need to access data, AFAIK.
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Doktoro ReichardAug 17 '13 at 19:19

The method in the article is making a "junction" which is essentially a hard link. Mounting a drive to an empty folder. I'm guessing you want to encrypt the partition not the entire drive. Should be possible using BitLocker.
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wolfo9999Aug 17 '13 at 19:25

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@DoktoroReichard Actually the drivers truecrypt uses for whole drive encryption are fairly fast, from what I have seen worst case 10% performance loss, but normally only 1 or 2%
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Scott ChamberlainAug 18 '13 at 3:51